Find a cystic fibrosis protein function using bioinformatics to study homologs in model organisms.
Say you're a researcher interested in cystic fibrosis, a recessive genetic disease that causes excessive amounts of fluid to gather in the lungs and other organs.
You've located the gene that causes the disease and can read the protein's amino acid sequence, but you don't know what the protein does.
BLAST is a computer program available online at the National Center for Biotechnology Information that allows you to search for similar nucleotide and amino acid sequences in other proteins. By looking at similar sequences with known functions, you can get clues to the function of your unknown protein.
The first step in using BLAST is picking the program and database to use. First, click on the Program button. Blastp works by comparing an amino acid sequence to other proteins, while Blastn works by comparing a nucleotide sequence to other genes.
Now click on the Database button. You can search all available sequences in all organisms by choosing "nr," or limit your search to human ESTs, Drosophila, or yeast.
You want to use your protein sequence to find any other similar sequences. Choose the appropriate configuration of program and database.
Searching a wide database will find similar proteins from a variety of organisms. Using the protein's sequence instead of the nucleotide sequence will locate similar proteins even if their nucleotide sequences differ.
The next step is to enter your data into the input box. If you're entering nucleotides, simply use the sequence of letters. If you're entering an amino
acid sequence, use the single-letter IUB/IUPAC code shown below.
You are searching the protein database, so you represent each amino acid with a single letter. Now that you have selected the program and database and
have entered your data, press the "Search" button to look for similar proteins.
Enter your input data here
The search comes back with hundreds of matches color-coded according to the amount of similarity. Red and pink matches are considered highly-related
Which protein(s) is the functional homolog to the human protein?
All proteins listed. (No, it is unlikely that all the proteins are homologs.)
The red-coded matches. (Yes, but there may be more.)
The red and pink-coded matches. (No, that is incorrect.)
Possibly one or more of the red and pink-coded matches. (This is correct)
Though the proteins are structurally similar, they may not perform the exact same function. This has to be determined experimentally.
Rolling your mouse over the top five lines in the results graph tells you what proteins have produced these matches.
After looking at the descriptions of the structural homologs, what is your best guess as to the function of the human protein?
Transports a small molecule in or out of cells. (That is correct)
Transports a small molecule within cells. (No, the homologs are all transmembrane transporters.)
Transports a peptide within cells. (No, the homologs are all transmembrane transporters.)
Transports a peptide in or out of cells. (No, the homologs are not just peptides transporters.)
Transports toxins. (No, the homologs are not just toxin transporters.)
All the proteins transport a small molecule, whether it's an ion or peptide. The location of the protein in the membrane tells you that it moves molecules in and/or out of the cell. Further studies revealed the protein transports chloride ions, so the protein was named Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).
Homolog alignments were inspected more closely for regions of high similarity. The following is a partial alignment of the CFTR protein sequence with a related protein.
Though every amino acid does not match, this entire area is highly conserved. Therefore, it probably performs a vital function. Researchers later found that the protein will not be delivered to the membrane when phenylalanine (F) is deleted. The result is cystic fibrosis.
If you searched for similar proteins using the nucleotide sequence instead, the similarity between sequences would ...
be exactly the same. (No, that is incorrect.)
increase. (No, that is incorrect.)
decrease. (That is correct.)
Most amino acids are encoded by several codons, so that the same protein sequence may be encoded by a different
nucleotide sequence. Therefore, you would expect the similarity between matches to decrease.
YOU'RE SO SMART!
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A human is a complicated organism, and it is considered unethical to do many kinds of experiments on human subjects. For these reasons, biologists often use simpler “model” organisms that are easy to keep and manipulate in the laboratory.